Fix extract master_fieldlist

Author: Steve Goldhaber

tools/cmip_namelists/chemistry.py

@@ -14,22 +14,37 @@
 
 ## chemistry diag pre- and post-fixes
 ## Each list entry is a pair of possible new chemistry names
-__CHEM_DIAG_PRE_POST = [('GS_', ''), ('AQ_', ''), ('AQ_', '_OCW'),
-                        ('sink_', ''), ('sink_', '_S'),
-                        ('CT_', ''), ('SF', ''), ('emis_', ''),
-                        ('D', 'CHM'), ('F', '_fvm'), ('TA', ''), ('TM', ''),
-                        ('VD', ''), ('', 'CONU'), ('', 'DDF'), ('', 'DDV'),
-                        ('', 'DTQ'), ('', 'GVF'), ('', 'INS'), ('', 'SBC'),
-                        ('', 'SBS'), ('', 'SF'), ('', 'SFSBC'), ('', 'SFSBD'),
-                        ('', 'SFSBS'), ('', 'SFSEC'), ('', 'SFSED'),
-                        ('', 'SFSES'), ('', 'SFSIC'), ('', 'SFSID'),
-                        ('', 'SFSIS'), ('', 'SFWET'), ('', 'SFWETC'),
-                        ('', 'SIC'), ('', 'SIS'), ('', 'TBF'), ('', 'WET'),
-                        ('', 'WETC'), ('', '_CHML'), ('', '_CHMP'),
-                        ('', '_SRF'), ('', '_fvm'), ('', '_mixnuc1'),
-                        ('', '_num'), ('', '_qneg3'), ('', '_qneg3_col'),
-                        ('', '_sfcoag1'), ('', '_sfcsiz3'), ('', '_sfcsiz4'),
-                        ('', '_sfgaex2')]
+__CHEM_DIAG_PRE_POST = [('GS_', ''),        ('AQ_', ''),       ('AQ_', '_OCW'),
+                        ('sink_', ''),      ('sink_', '_S'),   ('CT_', ''),
+                        ('SF', ''),         ('emis_', ''),     ('D', 'CHM'),
+                        ('F', '_fvm'),      ('TA', ''),        ('TM', ''),
+                        ('VD', ''),         ('', 'CONU'),      ('', 'DDF'),
+                        ('', 'DDV'),        ('', 'DTQ'),       ('', 'GVF'),
+                        ('', 'INS'),        ('', 'SBC'),       ('', 'SBS'),
+                        ('', 'SF'),         ('', 'SFSBC'),     ('', 'SFSBD'),
+                        ('', 'SFSBS'),      ('', 'SFSEC'),     ('', 'SFSED'),
+                        ('', 'SFSES'),      ('', 'SFSIC'),     ('', 'SFSID'),
+                        ('', 'SFSIS'),      ('', 'SFWET'),     ('', 'SFWETC'),
+                        ('', 'SIC'),        ('', 'SIS'),       ('', 'TBF'),
+                        ('', 'WET'),        ('', 'WETC'),      ('', '_CHML'),
+                        ('', '_CHMP'),      ('', '_SRF'),      ('', '_fvm'),
+                        ('', '_mixnuc1'),   ('', '_num'),      ('', '_qneg3'),
+                        ('', '_qneg3_col'), ('', '_sfcoag1'),  ('', '_sfcsiz3'),
+                        ('', '_sfcsiz4'),   ('', '_sfgaex2'),  ('', '_OCWDDF'),
+                        ('', '_OCWGVF'),    ('', '_OCWSFSBC'), ('', '_OCW'),
+                        ('', '_OCWSFSBS'),  ('', '_OCWSFSIC'),
+                        ('', '_OCWSFSIS'),  ('', '_OCWSFWET'), ('', '_OCWTBF'),
+                        ('', '_OCW_mixnuc1'),
+                        ('', '_OCWclcoagTend'),                ('', 'coagTend'),
+                        ('', 'condTend'),   ('', '_CLXF'),     ('', '_CMXF'),
+                        ('', '_XFRC'),      ('', 'clcoagTend'),
+                        ('DC', ''),         ('WD_A_', ''),     ('cb_', ''),
+                        ('cb_', '_OCW')]
+
+__ESM_FIXED_FIELDS = {'CO2_OCN', 'CO2_FFF', 'CO2_LND', 'CO2'}
+__ESM_DIAG_PRE_POST = [('', '_BOT'),       ('', '_fvm'),  ('', '_qneg3'),
+                       ('', '_qneg3_col'), ('F', '_fvm'), ('SF', ''),
+                       ('TA', ''),         ('TM', ''),    ('VD', '')]
 
 ## Find chem species in mo_sim_dat.F90
 __SOLSYM_RE = re.compile(r"solsym[(][: 0-9]+[)] = [(]/(.*)$")
@@ -107,6 +122,21 @@ def read_chem_species(chem_name):
 
     return species_list
 
+def all_diags_set(species_list, pre_post_list):
+    """Using a list of species names, <species_list>, create a set that
+    includes these names plus each name decorated by the pre- and post-patterns
+    from <pre_post_list>.
+    Return this set of strings.
+    """
+    diag_names = set()
+    for speci in species_list:
+        diag_names.add(speci)
+        for decor in pre_post_list:
+            diag_names.add(f"{decor[0]}{speci}{decor[1]}")
+        # end if
+    # end for
+    return diag_names
+
 def all_chem_names(chem_name=None):
     """Return a set containing all chemistry diagnostic names for one
     chemistry scheme (chem_name==None) or for all chemistry schemes
@@ -119,14 +149,15 @@ def all_chem_names(chem_name=None):
         all_chem_file = os.path.join(__MYDIR, "chemistry_fieldlist.txt")
         all_species = read_fieldname_file(all_chem_file)
     # end if
-    for chem_speci in all_species:
-        diag_names.add(chem_speci)
-        for decor in __CHEM_DIAG_PRE_POST:
-            diag_names.add(f"{decor[0]}{chem_speci}{decor[1]}")
-        # end if
-    # end for
+    diag_names = all_diags_set(all_species, __CHEM_DIAG_PRE_POST)
     return diag_names
 
+def all_emission_names():
+    """Return a set of all the diagnostic field names associated with the
+    CO2 emission-driven constituent fields, including CO2.
+    """
+    return all_diags_set(__ESM_FIXED_FIELDS, __ESM_DIAG_PRE_POST)
+
 ###############################################################################
 
 if __name__ == "__main__":

tools/cmip_namelists/extract_master_list.py

@@ -10,7 +10,7 @@
 import re
 import sys
 ## Local imports
-from chemistry import all_chem_names
+from chemistry import all_chem_names, all_emission_names
 
 _BEGIN_MASTER_LIST_RE = re.compile(r"[ ]*[*]+ MASTER FIELD LIST [*]+")
 _END_MASTER_LIST_RE = re.compile(r"[ ]*intht:nfmaster=")
@@ -45,7 +45,7 @@ def parse_diagnostic_fieldnames(logfiles, output_file):
 
     all_fieldnames = set()
     in_masterlist = False
-    chem_names = all_chem_names()
+    exclude_names = all_chem_names() | all_emission_names()
     linenum = 0
     for logfile in logfiles:
         with open(logfile, mode='r') as infile:
@@ -59,7 +59,7 @@ def parse_diagnostic_fieldnames(logfiles, output_file):
                         fieldmatch = _FIELDLINE_RE.match(line)
                         if fieldmatch is not None:
                             fldname = fieldmatch.group(1)
-                            if ('&IC' not in fldname) and (fldname not in chem_names):
+                            if ('&IC' not in fldname) and (fldname not in exclude_names):
                                 all_fieldnames.add(fldname)
                             # end if
                         else: